RetrogeneDB ID: retro_atha_21

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 5:22310857..22312681(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT5G54960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT4G33070
• Aliases: None
• Description: None

Sequence

>retro_atha_21
ATGGACACTAAGATCGGATCTATCGACGCGTGTAACCCGACCAACCACGATATCGGCGGTCCTCCAAACGGCGGAGTCTC
CACCGTTCAAAACACAAGTCCACTTCACTCCACCACCGTCAGCCCCTGCGACGCGACTCTTGGCCGTTACCTAGCAAGAC
GGTTAGTCGAAATCGGCGTCACCGATGTCTTCTCCGTTCCTGGTGATTTCAACCTGACGCTTCTCGATCACCTAATCGCC
GAACCAAACCTCAAGCTGATCGGTTGCTGCAACGAGCTTAACGCCGGATACGCTGCTGACGGTTACGCTAGATCTCGCGG
TGTTGGTGCGTGCGTCGTTACGTTCACCGTCGGTGGATTGAGTGTTCTGAATGCGATCGCCGGTGCTTACAGTGAGAATC
TGCCTCTGATTTGCATCGTCGGTGGTCCAAACTCCAACGATTACGGTACCAATAGGATTCTTCATCATACAATTGGTTTA
CCTGATTTCACTCAAGAGCTTAGGTGTTTTCAAGCTGTTACTTGTTTTCAAGCTGTGATTAATAACTTAGAAGAGGCTCA
TGAACTTATCGATACTGCGATTTCAACTGCTTTGAAAGAAAGCAAACCTGTTTATATCAGTATCAGCTGTAATTTACCGG
CGATTCCTCTTCCGACGTTTAGTCGTCATCCTGTTCCGTTCATGCTTCCGATGAAGGTTAGCAATCAGATTGGTTTAGAT
GCGGCGGTGGAGGCAGCTGCTGAGTTCTTGAACAAAGCTGTGAAGCCAGTTCTTGTTGGTGGGCCGAAAATGCGGGTTGC
GAAAGCCGCGGATGCTTTTGTTGAGCTTGCTGATGCTTCTGGCTATGGTCTTGCTGTGATGCCTTCTGCTAAAGGACAAG
TACCTGAGCATCACAAGCATTTTATAGGGACGTATTGGGGAGCTGTGAGTACAGCTTTTTGTGCTGAAATCGTTGAATCT
GCGGATGCTTATCTGTTTGCAGGTCCGATTTTCAACGATTACAGTTCTGTTGGGTATTCTCTGCTTCTCAAGAAGGAGAA
GGCAATCATCGTTCAGCCTGATCGGGTTACTATCGGTAACGGACCTGCGTTTGGATGTGTTCTTATGAAGGATTTTCTAA
GCGAGTTGGCTAAACGAATTAAGCACAACAACACTTCTTATGAGAATTATCACAGGATCTATGTCCCAGAAGGAAAGCCT
TTGAGAGATAACCCGAATGAGTCTTTGAGGGTTAATGTACTGTTCCAACACATTCAGAATATGCTCTCTTCTGAGTCTGC
TGTGCTTGCTGAGACAGGAGATTCCTGGTTCAACTGTCAGAAGCTGAAGCTCCCTGAAGGATGCGGTTACGAATTCCAAA
TGCAGTACGGATCAATTGGCTGGTCAGTGGGTGCTACTCTAGGCTATGCTCAAGCCATGCCAAACAGGCGTGTCATTGCT
TGTATTGGAGATGGTAGTTTCCAGGTAACCGCACAGGATGTATCTACGATGATACGGTGTGGGCAAAAGACCATAATCTT
CCTCATCAACAACGGAGGCTACACCATTGAGGTGGAAATTCACGATGGTCCTTACAATGTCATAAAGAACTGGAACTACA
CAGCTTTTGTTGAGGCCATACACAATGGAGAAGGAAAATGCTGGACTGCCAAGGTGAGATGCGAGGAGGAGTTAGTGAAA
GCAATCAACACGGCAACCAATGAGGAAAAAGAGAGCTTTTGTTTCATTGAAGTGATAGTGCACAAAGACGATACAAGCAA
GGAACTTTTGGAGTGGGGCTCTAGAGTCTCTGCTGCTAATAGTCGTCCCCCAAATCCGCAGTAG

Alignment

ORF - retro_atha_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTKIGSIDDCKPTNGDVCSPTNGTVATIHNSVPSSAITINYCDATLGRHLARRLVQAGVTDVFSVPGDF
          MDTKIGSID.C.PTN.D...P.NG.V.T..N..P....T...CDATLGR.LARRLV..GVTDVFSVPGDF
Retrocopy MDTKIGSIDACNPTNHDIGGPPNGGVSTVQNTSPLHSTTVSPCDATLGRYLARRLVEIGVTDVFSVPGDF

Parental  NLTLLDHLMAEPDLNLIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV
          NLTLLDHL.AEP.L.LIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV
Retrocopy NLTLLDHLIAEPNLKLIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV

Parental  GGPNSNDYGTNRILHHTIGLPDFSQELRCFQTVTCYQAVVNNLDDAHEQIDKAISTALKESKPVYISVSC
          GGPNSNDYGTNRILHHTIGLPDF.QELRCFQ.VTC.QAV.NNL..AHE.ID.AISTALKESKPVYIS.SC
Retrocopy GGPNSNDYGTNRILHHTIGLPDFTQELRCFQAVTCFQAVINNLEEAHELIDTAISTALKESKPVYISISC

Parental  NLAAIPHHTFSRDPVPFSLAPRLSNKMGLEAAVEATLEFLNKAVKPVMVGGPKLRVAKACDAFVELADAS
          NL.AIP..TFSR.PVPF.L....SN..GL.AAVEA..EFLNKAVKPV.VGGPK.RVAKA.DAFVELADAS
Retrocopy NLPAIPLPTFSRHPVPFMLPMKVSNQIGLDAAVEAAAEFLNKAVKPVLVGGPKMRVAKAADAFVELADAS

Parental  GYALAMMPSAKGFVPEHHPHFIGTYWGAVSTPFCSEIVESADAYIFAGPIFNDYSSVGYSLLLKKEKAIV
          GY.LA.MPSAKG.VPEHH.HFIGTYWGAVST.FC.EIVESADAY.FAGPIFNDYSSVGYSLLLKKEKAI.
Retrocopy GYGLAVMPSAKGQVPEHHKHFIGTYWGAVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSLLLKKEKAII

Parental  VQPDRITVANGPTFGCILMSDFFRELSKRVKRNETAYENYHRIFVPEGKPLKCESREPLRVNTMFQHIQK
          VQPDR.T..NGP.FGC.LM.DF..EL.KR.K.N.T.YENYHRI.VPEGKPL.....E.LRVN..FQHIQ.
Retrocopy VQPDRVTIGNGPAFGCVLMKDFLSELAKRIKHNNTSYENYHRIYVPEGKPLRDNPNESLRVNVLFQHIQN

Parental  MLSSETAVIAETGDSWFNCQKLKLPKGCGYEFQMQYGSIGWSVGATLGYAQASPEKRVLAFIGDGSFQVT
          MLSSE.AV.AETGDSWFNCQKLKLP.GCGYEFQMQYGSIGWSVGATLGYAQA.P..RV.A.IGDGSFQVT
Retrocopy MLSSESAVLAETGDSWFNCQKLKLPEGCGYEFQMQYGSIGWSVGATLGYAQAMPNRRVIACIGDGSFQVT

Parental  VQDISTMLRNGQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEGNCWTAKVRYEEELVE
          .QD.STM.R.GQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYT..V.AIHNGEG.CWTAKVR.EEELV.
Retrocopy AQDVSTMIRCGQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTAFVEAIHNGEGKCWTAKVRCEEELVK

Parental  AITTATTEKKDCLCFIEVILHKDDTSKELLEWGSRVSAANSRPPNPQ
          AI.TAT.E.K...CFIEVI.HKDDTSKELLEWGSRVSAANSRPPNPQ
Retrocopy AINTATNEEKESFCFIEVIVHKDDTSKELLEWGSRVSAANSRPPNPQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_21 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G33070	1 retrocopy	retro_atha_21 ,
Brassica oleracea	Bo2g001320	1 retrocopy	retro_bole_3,
Brassica rapa	Bra028896	1 retrocopy	retro_brap_2,
Arabidopsis lyrata	fgenesh2_kg.7__814__AT4G33070.1	1 retrocopy	retro_alyr_26,